Peptide variability and signatures associated with disease progression in CSF collected longitudinally from ALS patients

Abstract

We employ shotgun proteomics and data-independent acquisition (DIA) mass spectrometry to analyze cerebrospinal fluid longitudinally collected from 14 amyotrophic lateral sclerosis (ALS) patients (8 males and 6 females). We perform three main analyses of these data: (1) examine the intra- and inter-patient protein variability in CSF; (2) explore the association of inflammation with rate of disease progression; and (3) develop a mixed-effects model to best explain the decrease in ALS-Functional Rating Scale (ALS-FRS) score. Overall, the CSF protein abundances are tightly regulated with the intra-individual variability contributing just 4% to the overall variance. In four patients, a moderately significant correlation (p < 0.1) was observed between inflammation and rate of disease progression. Using a least absolute shrinkage and selection operator (LASSO) variable selection, we selected 55 viable peptides for mathematical modeling via a linear mixed-effects regression. We then employed forward selection to generate a final model by minimizing Akaike’s information criterion (AIC). The final model utilized changes in abundance from 28 peptides as fixed effects to model progression of the disease in these patients. These peptides were from proteins involved in stress response and innate immunity.

Graphical abstract

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Abbreviations

ABC:

Ammonium bicarbonate

AIC:

Akaike’s information criterion

ALS:

Amyotrophic lateral sclerosis

ALS-FRS:

ALS-Functional Rating Scale

CHI3L1:

Chitinase-3-like protein 1

CHI3L2:

Chitinase-3-like protein 2

CHIT1:

Chitotriosidase

CSF:

Cerebrospinal fluid

DDA:

Data-dependent acquisition

DIA:

Data-independent acquisition

DTT:

Dithiothreitol

IAM:

Iodoacetamide

LASSO:

Least absolute shrinkage and selection operator

SDC:

Sodium deoxycholate

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Acknowledgments

We gratefully acknowledge the NEALS Biorepository for providing all the biofluids from ALS patients used in this study. We also acknowledge the ALS Association (grant #19-SI-458) for the funding of this project. All mass spectrometry measurements were made in the Molecular Education, Technology, and Research Innovation Center (METRIC) at NC State University.

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Correspondence to Michael S. Bereman.

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The NEALS Biorepository collects and stores cryopreserved CSF from consenting patients, who have been worked up in neurological detail, at the NEALS-affiliated clinical sites. The sample collection and the corresponding clinical information storage and sharing are performed under approved IRB protocols and in accordance with HIPPA.

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The authors declare that they have no conflicts of interest.

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Mellinger, A.L., Griffith, E.H. & Bereman, M.S. Peptide variability and signatures associated with disease progression in CSF collected longitudinally from ALS patients. Anal Bioanal Chem (2020). https://doi.org/10.1007/s00216-020-02765-8

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Keywords

  • Amyotrophic lateral sclerosis
  • Cerebrospinal fluid
  • Longitudinal modeling
  • Proteomics
  • Biomarker